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A Comparative Study for the Accuracy of Three Molecular Docking Programs Using HIV-1 Protease Inhibitors as a Model
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Flexible molecular docking is a computational method of structure-based drug design to evaluate binding interactions between receptor and ligand and identify the ligand conformation within the receptor pocket. Currently, various molecular docking programs are extensively applied; therefore, realizing accuracy and performance of the various docking programs could have a significant value. In this comparative study, the performance and accuracy of three widely used non-commercial docking software (AutoDock Vina, 1-Click Docking, and UCSF DOCK) was evaluated through investigations of the predicted binding affinity and binding conformation of the same set of small molecules (HIV-1 protease inhibitors) and a protein target HIV-1 protease enzyme. The tested sets are composed of eight receptor-ligand complexes with high resolution crystal structures downloaded from Protein Data Bank website. Molecular dockings were applied between approved HIV-1 protease inhibitors and the HIV-1 protease using AutoDock Vina, 1-Click Docking, and DOCK6. Then, docking poses of the top-ranked solution was realized using UCSF Chimera. Furthermore, Pearson correlation coefficient (r) and coefficient of determination (r2) between the experimental results and the top scored docking results of each program were calculated using Graphpad prism V9.2. After comparing saquinavir top scored binding poses of each docking program with the crystal structure, various conformational changes were observed. Moreover, according to the relative comparison between the top ranked calculated ?Gbinding values against the experimental results, r2 value of AutoDock Vina, 1-Click Docking, and DOCK6 were 0.65, 0.41, and 0.005, respectively. The outcome of this study shows that the top scored binding free energy could not produce the best pose prediction. In addition, AutoDock Vina results have the highest correlation with the experimental results.

 

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Publication Date
Wed Jun 03 2020
Journal Name
Political Sciences Journal
Transitional justice: a study of the concept and mechanisms
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The concept of transitional justice is newly emerging, as it was mainly associated with addressing issues of serious breaches and abuses of human rights during conflicts and situations resulting from violence and the use of force in societies that are in the process of democratization, as transitional justice aims primarily to restore civil peace and rebuild institutions The state needs multidimensional justice: a judicial system that achieves the rule of law, corrective restoration of the wounds of the past, and a distributive characteristic of the redistribution of wealth.

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Publication Date
Fri Aug 30 2019
Journal Name
Journal Of The College Of Education For Women
A Cognitive Linguistic Study of the English Preposition 'in'
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The present study aims at analyzing the polysemy of the English preposition in from the cognitive linguistic (CL) point of view using Evans' and Tyler's approach (2003). The perplexity faced by Iraqi second language learners (L2) due to the multi-usages of this preposition has motivated the researcher to conduct this study. Seventy-six second year university students participated in this experimental study. The data of the pre-test and post-test were analyzed by SPSS statistical editor. The results have shown the following: First, a progress of more than (0.05≤) has been detected as far as students' understanding of the multiple usages of the preposition in is concerned. Second, the results of the questionnaire have s

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Publication Date
Thu Sep 10 2020
Journal Name
Journal Of Advances In Mathematics
A Study of The Density Property in Module Theory
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In this paper, there are two main objectives. The first objective is to study the relationship between the density property and some modules in detail, for instance; semisimple and divisible modules. The Addition complement has a good relationship with the density property of the modules as this importance is highlighted by any submodule N of M has an addition complement with Rad(M)=0. The second objective is to clarify the relationship between the density property and the essential submodules with some examples. As an example of this relationship, we studied the torsion-free module and its relationship with the essential submodules in module M.

Publication Date
Sun Dec 01 2013
Journal Name
Political Sciences Journal
Yemeni political system: a study of the internal variables
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النظام السياسي اليمني : دراسة في المتغيرات الداخلية

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Publication Date
Thu Jan 01 2015
Journal Name
Political Sciences Journal
Fiscal federalism: a study of the concept and models
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يمثل الأخذ بالنظام الفيدرالي أطاراً تنظيمياً لشكل الدولة و مرحلة تحول مهمة في بنية الدولة العامة في مختلف مجالاتها، فالانتقال من المركزية في أدارة الشؤون العامة للدولة الى النمط الفيدرالي يمثل تحولا بنيوياً وسيكولوجياً ،حيث يكون هنالك توزيع مكاني - عمودي للسلطة والثروة بين الوحدات المكونة للدولة بشكل يختلف كليا عن الحالة المركزية، ونجد صور تنظيمية عديدة تتأسس ضمن اطار الفيدرالية العام ،

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Publication Date
Fri Feb 08 2019
Journal Name
Iraqi Journal Of Laser
Writing of a Bragg Grating on a D-shaped Optical Fiber Using the KrF Excimer Laser
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Fiber Bragg Grating has many advantages where it can be used as a temperature sensor, pressure sensor or even as a refractive index sensor. Designing each of this fiber Bragg grating sensors should include some requirements. Fiber Bragg grating refractive index sensor is a very important application. In order to increase the sensing ability of fiber Bragg gratings, many methods were followed. In our proposed work, the fiber Bragg grating was written in a D-shaped optical fiber by using a phase mask method with KrFexcimer. The resultant fiber Bragg grating has a high reflectivity 99.99% with a Bragg wavelength of 1551.2 nm as a best result obtained from a phase mask with a grating period of 1057 nm. In this work it was found that the rota

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Publication Date
Sat Jan 01 2022
Journal Name
Journal Of Algebraic Statistics
The effect of compound exercises for the arm least used in developing the accuracy of the passing skill of the handball for ages (15-17) years
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Publication Date
Sat Jun 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
Requirements of stress tests model and the possibility to apply in Iraqi banks exploratory study of the views of a sample of staff in the central Bank of Iraq .
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Abstract

This research attempt to explain the essential aspects of one important model in management of Bank risks , that is (stress testing) , which increase the concentrate on it resulting the negative affects of Global financial crisis that it accuar in 2008 to study the application possibilities in iraqian banks to enhancing the safety and financial soundness Becuase the classical tools  in Risk management don’t give clear image on Banks ability  in facing risks, hence the Basel committee on Banking supervision focusing in agreement of Basel 2,3 on stress testing when it doing the internal capital adequacy assessment process (ICAAP) .

To achieving the reseach obje

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Publication Date
Wed Mar 18 2020
Journal Name
Baghdad Science Journal
Spectrophotometric and Reverse Flow Injection Method Determination of Nitrazepam in Pharmaceuticals Using O-Coumaric Acid as a New Chromogenic Reagent
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            A spectrophotometric- reverse flow injection analysis (rFIA) method has been proposed for the   determination of Nitrazepam (NIT) in pure and pharmaceutical preparations. The method is based upon the coupling reaction of NIT with a new reagent O-Coumaric acid (OCA) in the presence of sodium periodate in an aqueous solution. The blue color product was measured at 632 nm. The variation (chemical and physical parameters) related with reverse flow system were estimated. The linearity was over the range 15 - 450 µg/mL of NIT with detection limits and limit of quantification of 3.425 and 11.417 µg mL-1 NIT,respectively. The sample throughput of 28 samples

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Publication Date
Sun Jun 26 2022
Journal Name
International Journal Of Corrosion And Scale Inhibition
Theoretical and experimental studies of copper(II) and nickel(II) complexes derived from the ligand N-benzyl benzimidazole as corrosion inhibitors in ionic and bacterial media
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